TABLE 2.

All known HERV-K (HML-2) proviruses and their RPKM values as detected in PBLs after HIV-1 Tat or vehicle-alone treatment using RNA-Seq^a

Chromosome	Length (kb)	Locus	Name and alternative name(s)	Unique RPKM value by treatment
				Tat	Vehicle
1	6,104	1p36.21a	1p36.21a	0.0000	0.0000
1	9,521	1p36.21b	K(OLDAL023753), K6, K76	0.0000	0.0000
1	9,392	1p36.21c	K6, K76	0.0000	0.0000
1	1,238	1p34.3	1p34.3	0.0000	0.0000
1	6,372	1p31.1	K4, K116, ERVK-1	0.2416	0.1461
1	3,077	1q21.3	1q21.3	3.0075	0.8425
1	9,179	1q22	K102, K(C1b), K50a, ERVK-7	0.7907	0.2809
1	9,231	1q23.3	K110, K18, K(C1a), ERVK-18	0.4454	0.2110
1	5,655	1q24.1	K12	0.0060	0.0000
1	4,179	1q32.2	1q32.2	0.0000	0.0514
1	2,178	1q43	1q43	0.0000	0.0000
2	2,671	2q21.1	2q21.1	0.0000	0.0590
3	6,890	3p25.3	K11, ERVK-2	0.0123	0.0270
3	8,685	3p12.3	3p12.3	0.1286	0.0016
3	9,122	3q12.3	K(II), ERVK-5	1.8324	0.7050
3	8,803	3q13.2	K106, K(C3), K68, ERVK-3	0.0058	0.0049
3	9,114	3q21.2	K(I), ERVK-4	0.0835	0.0566
3	3,919	3q24	ERVK-13	0.0000	0.0000
3	9,179	3q27.2	K50b, K117, ERVK-11	0.0424	0.0328
4	4,470	4p16.3a	4p16.3a	0.0114	0.0384
4	8,562	4p16.3b	K77	0.0553	0.0736
4	9,560	4p16.1a	K17b	0.0637	0.0839
4	9,062	4p16.1b	K50c	0.5227	0.0980
4	5,514	4q13.2	4q13.2	0.0000	0.0000
4	2,422	4q32.1	4q32.1	0.1746	0.0000
4	7,228	4q32.3	K5, ERVK-12	0.0000	0.0119
4	7,287	4q35.2	4q35.2	0.0720	0.0609
5	9,091	5p13.3	K104, K50d	0.0037	0.0016
5	9,843	5p12	K8	0.0017	0.0422
5	7,712	5q33.2	K18b	0.0088	0.0316
5	9,179	5q33.3	K107/K10, K(C5), ERVK-10	0.0608	0.0312
6	10,368	6p22.1	K(OLDAL121932), K69, K20	0.0000	0.0000
6	9,958	6p21.1	K(OLDAL035587), KOLD35587	0.0374	0.0302
6	4,808	6p11.2	K23	0.0035	0.0923
6	9,064	6q14.1	K109, K(C6), ERVK-9	0.0000	0.0032
6	2,825	6q25.1	6q25.1	0.0180	0.0862
7	9,471	7p22.1a	K108L, K(HML.2-HOM), K(C7), ERVK-6	0.0000	0.0030
7	9,470	7p22.1b	K108R, ERVK-6, HERV-K (HML-2).HOM	0.0518	0.0212
7	2,695	7q11.21	7q11.21	0.0000	0.0000
7	4,897	7q22.2	ERVK-14	0.1244	0.0000
7	4,977	7q34	K(OLDAC004979), ERVK-15	1.7302	0.3914
8	9,462	8p23.1a	K115, ERVK-8	0.1037	0.0378
8	1,025	8p23.1b	K27	0.0000	0.0000
8	9,527	8p23.1c	8p23.1c	0.0586	0.0060
8	9,515	8p23.1d	KOLD130352	0.0658	0.0030
8	8,738	8p22	8p22	0.0174	0.0344
8	8,011	8q11.1	K70, K43	0.0000	0.0536
8	3,087	8q24.3a	8q24.3a	0.0000	0.0000
8	7,563	8q24.3b	K29	0.1633	0.0170
9	7,221	9q34.11	K31	0.3889	0.1686
9	9,462	9q34.3	K30	0.0054	0.0212
10	7,526	10p14	K(C11a), K33, ERVK-16	0.0090	0.0837
10	981	10p12.1	K103, K(C10)	0.0172	0.0000
10	7,147	10q24.2	ERVK-17, c10_B	0.0071	0.0040
11	9,553	11p15.4	K7	0.3507	0.0825
11	5,748	11q12.1	11q12.1	0.0000	0.0050
11	14,600	11q12.3	K(OLDAC004127)	0.1506	0.0275
11	9,465	11q22.1	K(C11c), K36, K118, ERVK-25	0.0018	0.0076
11	9,159	11q23.3	K(C11b), K37, ERVK-20	0.0092	0.0407
12	9,662	12p11.1	K50e	0.0000	0.0163
12	968	12q13.2	12q13.2	0.0000	0.0000
12	9,456	12q14.1	K(C12), K41, K119, ERVK-21	0.0000	0.0121
12	1,482	12q24.11	12q24.11	0.0114	0.0000
12	6,012	12q24.33	K42	0.0338	0.0048
14	3,496	14q11.2	K(OLDAL136419), K71	0.5904	0.2048
14	2,881	14q32.33	14q32.33	0.0000	0.0000
15	3,344	15q25.2	15q25.2	0.0000	0.0000
16	1,501	16p13.3	K(OLDAC004034)	0.3156	0.0286
16	2,668	16p11.2	16p11.2	0.0254	0.0000
17	6,862	17p13.1	17p13.1	0.0099	0.0605
19	2,542	19p13.3	ERVK-22	0.0000	0.0056
19	10,112	19p12a	K52	0.0033	0.0269
19	6	19p12b	K113 (potential insertion site, 6 bp long)	0.0000	0.0000
19	6,737	19p12c	K51	0.0075	0.0000
19	8,863	19q11	K(C19), ERVK-19	0.0630	0.0259
19	4,227	19q13.12a	19q13.12a	0.1201	0.0000
19	9,517	19q13.12b	K50F	0.9475	0.5252
19	4,317	19q13.41	19q13.41	0.1254	0.0597
19	5,696	19q13.42	LTR13	0.0149	0.0503
20	9,634	20q11.22	K(OLDAL136419), K59	0.0386	0.0253
21	8,046	21q21.1	K60, ERVK-23	0.0000	0.0285
22	9,120	22q11.21	K101, K(C22), ERVK-24	0.0519	0.0031
22	8,880	22q11.23	K(OLDAP000345), KOLD345	0.0038	0.0500
X	2,505	Xq11.1	Xq11.1	0.0135	0.1029
X	2,052	Xq12	Xq12	0.0000	0.0000
X	2,399	Xq28a	K63	0.0000	0.0000
X	7,340	Xq28b	K63	0.0000	0.0020
Y	6,943	Yp11.2	Yp11.2	0.0000	0.0000
Y	3,198	Yq11.23a	Yq11.23a	0.0000	0.0000
Y	3,199	Yq11.23b	Yq11.23b	0.0000	0.0000

^aThe different names shown represent alternative ways to refer to the same virus based on the literature. Tat or vehicle unique RPKM values are the reads that had a single unique genomic alignment, mapping to a particular provirus, not shared with any other known provirus.